When you iPod is plugged in with iTunes open, look in the left sidebar under 'Devices' and your iPod will be listed. Click on its name and then you will see the Summary tab. There is a tab for Applications, click on that and then choose the syncing options as you like.
If you are deleting Apps on the touch and not changing the settings in iTunes then the Apps will be re-synced back on your touch when its next plugged in.